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Gremlin: An Interactive Visualization Model for Analyzing Genomic Rearrangements
November/December 2010 (vol. 16 no. 6)
pp. 918-926
ASCII Text
x 
 
Trevor O'Brien, Anna Ritz, Benjamin Raphael, David Laidlaw, "Gremlin: An Interactive Visualization Model for Analyzing Genomic Rearrangements," IEEE Transactions on Visualization and Computer Graphics, vol. 16, no. 6, pp. 918-926, November/December, 2010.
 
 
BibTex
x
 
@article{ 10.1109/TVCG.2010.163,
author = {Trevor O'Brien and Anna Ritz and Benjamin Raphael and David Laidlaw},
title = {Gremlin: An Interactive Visualization Model for Analyzing Genomic Rearrangements},
journal ={IEEE Transactions on Visualization and Computer Graphics},
volume = {16},
number = {6},
issn = {1077-2626},
year = {2010},
pages = {918-926},
doi = {http://doi.ieeecomputersociety.org/10.1109/TVCG.2010.163},
publisher = {IEEE Computer Society},
address = {Los Alamitos, CA, USA},
}
 
 
RefWorks Procite/RefMan/Endnote
x 
 
TY - JOUR
JO - IEEE Transactions on Visualization and Computer Graphics
TI - Gremlin: An Interactive Visualization Model for Analyzing Genomic Rearrangements
IS - 6
SN - 1077-2626
SP918
EP926
EPD - 918-926
A1 - Trevor O'Brien,
A1 - Anna Ritz,
A1 - Benjamin Raphael,
A1 - David Laidlaw,
PY - 2010
KW - Information visualization
KW - bioinformatics
KW - insight-based evaluation.
VL - 16
JA - IEEE Transactions on Visualization and Computer Graphics
ER -
 
Trevor O'Brien, Brown University
Anna Ritz, Brown University
Benjamin Raphael, Brown University
David Laidlaw, Brown University
In this work we present, apply, and evaluate a novel, interactive visualization model for comparative analysis of structural variants and rearrangements in human and cancer genomes, with emphasis on data integration and uncertainty visualization. To support both global trend analysis and local feature detection, this model enables explorations continuously scaled from the high-level, complete genome perspective, down to the low-level, structural rearrangement view, while preserving global context at all times. We have implemented these techniques in Gremlin, a genomic rearrangement explorer with multi-scale, linked interactions, which we apply to four human cancer genome data sets for evaluation. Using an insight-based evaluation methodology, we compare Gremlin to Circos, the state-of-the-art in genomic rearrangement visualization, through a small user study with computational biologists working in rearrangement analysis. Results from user study evaluations demonstrate that this visualization model enables more total insights, more insights per minute, and more complex insights than the current state-of-the-art for visual analysis and exploration of genome rearrangements.

[1] M. Bostock and J. Heer, Protovis: A graphical toolkit for visualization. IEEE Transactions on Visualization and Computer Graphics, 15 (6): 1121–1128, 2009.
[2] K. Chen, J. W. Wallis, M. D. McLellan, D. E. Larson, J. M. Kalicki, C. S. Pohl, S. D. McGrath, M. C. Wendl, Q. Zhang, D. P. Locke, X. Shi, R. S. Fulton, T. J. Ley, R. K. Wilson, L. Ding, and E. R. Mardis, BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nature Methods, 6 (9): 677–681, August 2009.
[3] A. Esteban-Marcos, A. E. Darling, and M. A. Ragan, Seevolution. Bioin-formatics, 25 (7): 960–961, 2009.
[4] D. Karolchik, G. Bejerano, A. S. Hinrichs, R. M. Kuhn, W. Miller, K. R. Rosenbloom, A. S. Zweig, D. Haussler, and W. J. Kent, Comparative genomic analysis using the UCSC genome browser. 395, November 2007.
[5] M. Krzywinski, J. Schein, A. a. Birol, J. Connors, R. Gascoyne, D. Hors-man, S. J. Jones, and M. A. Marra, Circos: An information aesthetic for comparative genomics. Genome Research, 19 (9): 1639–1645, September 2009.
[6] M. Meyer, T. Munzner, and H. Pfister, MizBee: A multiscale synteny browser. IEEE Transactions on Visualization and Computer Graphics, 15 (6): 897–904, 2009.
[7] C. B. Nielsen, M. Cantor, I. Dubchak, D. Gordon, and T. Wang, Visualizing genomes: Techniques and challenges. Nature Methods, 7 (3 Suppl), March 2010.
[8] C. North, Toward measuring visualization insight. IEEE Comput. Graph. Appl., 26 (3): 6–9, 2006.
[9] E. D. Pleasance, R. K. Cheetham, P. J. Stephens, D. J. McBride, S. J. Humphray, C. D. Greenman, I. Varela, M.-L. Lin, G. R. OrdÃ?Ãez, G. R. Bignell, K. Ye, J. Alipaz, M. J. Bauer, D. Beare, A. Butler, R. J. Carter, L. Chen, A. J. Cox, S. Edkins, P. I. Kokko-Gonzales, N. A. Gormley, R. J. Grocock, C. D. Haudenschild, M. M. Hims, T. James, M. Jia, Z. Kingsbury, C. Leroy, J. Marshall, A. Menzies, L. J. Mudie, Z. Ning, T. Royce, O. B. Schulz-Trieglaff, A. Spiridou, L. A. Stebbings, L. Szajkowski, J. Teague, D. Williamson, L. Chin, M. T. Ross, P. J. Campbell, D. R. Bentley, P. A. Futreal, and M. R. Stratton, A comprehensive catalogue of somatic mutations from a human cancer genome. Nature, advance online publication, December 2009.
[10] P. Saraiya, C. North, and K. Duca, An insight-based methodology for evaluating bioinformatics visualizations. IEEE Transactions on Visualization and Computer Graphics, 11 (4): 443–456, 2005.
[11] S. Sindi, E. Helman, A. Bashir, and B. J. Raphael, A geometric approach for classification and comparison of structural variants. Bioinformatics (Oxford, England), 25 (12): i222–230, June 2009.
[12] A. Sinha and J. Meller, Cinteny: Flexible analysis and visualization of synteny and genome rearrangements in multiple organisms. BMC Bioinformatics, 8 (1): 82, 2007.
[13] E. R. Tufte, The Visual Display of Quantitative Information. Graphics Press, Cheshire, Connecticut 2001.
[14] J. Yang, J. Wang, Z.-J. Yao, Q. Jin, Y. Shen, and R. Chen, Genome-Comp: A visualization tool for microbial genome comparison. Journal of Microbiological Methods, 54 (3): 423–426, 2003.

Index Terms:
Information visualization, bioinformatics, insight-based evaluation.
Citation:
Trevor O'Brien, Anna Ritz, Benjamin Raphael, David Laidlaw, "Gremlin: An Interactive Visualization Model for Analyzing Genomic Rearrangements," IEEE Transactions on Visualization and Computer Graphics, vol. 16, no. 6, pp. 918-926, Nov.-Dec. 2010, doi:10.1109/TVCG.2010.163
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